Genome-wide analysis of RNA-binding proteins co-expression with alternative splicing events in mitral valve prolapse

Meng Zhao; Jingxin Zhou; Yihu Tang; Mingzhu Liu; Yawei Dai; Hui Xie; Zihao Wang; Liang Chen; Yanhu Wu

doi:10.3389/fimmu.2023.1078266

Genome-wide analysis of RNA-binding proteins co-expression with alternative splicing events in mitral valve prolapse

Front Immunol. 2023 Apr 26:14:1078266. doi: 10.3389/fimmu.2023.1078266. eCollection 2023.

Authors

Meng Zhao¹, Jingxin Zhou¹, Yihu Tang¹, Mingzhu Liu¹, Yawei Dai¹, Hui Xie¹, Zihao Wang¹, Liang Chen¹, Yanhu Wu¹

Affiliation

¹ First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.

Abstract

Objectives: We investigated the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of mitral valve prolapse (MVP).

Methods: For RNA extraction, we obtained peripheral blood mononuclear cells (PBMCs) from five patients with MVP, with or without chordae tendineae rupture, and five healthy individuals. High-throughput sequencing was used for RNA sequencing (RNA-seq). Differentially expressed genes (DEGs) analysis, alternative splicing (AS) analysis, functional enrichment analysis, co-expression of RBPs, and alternative splicing events (ASEs) analysis were conducted.

Results: The MVP patients exhibited 306 up-regulated genes and 198 down-regulated genes. All down- and up-regulated genes were enriched in both Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, MVP was closely associated with the top 10 enriched terms and pathways. In MVP patients, 2,288 RASEs were found to be significantly different, and four suitable RASEs (CARD11 A3ss, RBM5 ES, NCF1 A5SS, and DAXX A3ss) were tested. We identified 13 RNA-binding proteins (RBPs) from the DEGs and screened out four RBPs (ZFP36, HSPA1A, TRIM21, and P2RX7). We selected four RASEs based on the co-expression analyses of RBPs and RASEs, including exon skipping (ES) of DEDD2, alternative 3' splice site (A3SS) of ETV6, mutually exclusive 3'UTRs (3pMXE) of TNFAIP8L2, and A3SS of HLA-B. Furthermore, the selected four RBPs and four RASEs were validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and showed high consistency with RNA sequencing (RNA-seq).

Conclusion: Dysregulated RBPs and their associated RASEs may play regulatory roles in MVP development and may therefore be used as therapeutic targets in the future.

Keywords: RNA sequencing; RNA-binding protein; alternative splicing; genome-wide analysis; mitral valve prolapse.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing
Cell Cycle Proteins / genetics
DNA-Binding Proteins / genetics
Humans
Leukocytes, Mononuclear
Mitral Valve Prolapse* / genetics
RNA-Binding Proteins / genetics
RNA-Seq
Tumor Suppressor Proteins / genetics

Substances

RNA-Binding Proteins
RBM5 protein, human
DNA-Binding Proteins
Cell Cycle Proteins
Tumor Suppressor Proteins

Grants and funding

This work was funded in part by the Jiangsu Provincial Health Commission’s medical scientific research project (ZD2021046) and the National Scientific Foundation of China (NSFC, grant nos.81700340).